Plant Hormone Signaling Pathways Research Articles

Physiological and transcriptome analysis reveals the mechanism of Gymnocarpos przewalskii response to drought stress

BackgroundGymnocarpos przewalskii Bunge ex Maxim. (G. przewalskii) is an endangered xerophytic shrub that plays a crucial role as a source of forage in the Alxa Desert. However, there is limited understanding regarding the forage quality of G. przewalskii and its response to drought. This study aimed to evaluate the forage quality of G. przewalskii and investigate the physiological and transcriptomic changes in G. przewalskii response to drought stress.ResultsThe ash, fat, crude protein, lignin, crude fiber, acid detergent fiber, and neutral detergent fiber contents in G. przewalskii twigs were 10.61%, 1.85%, 5.68%, 7.08%, 21.23%, 42.16%, and 58.42%, respectively. In contrast, these ingredients in its leaves were 20.39%, 0.92%, 11.96%, 2.40%, 17.51%, 14.29% and 20.26%, respectively. Osmotic stress led to a reduction in chlorophyll levels and an increase in malondialdehyde content. Levels of hydrogen peroxide and oxygen free radicals remained relatively stable under osmotic stress. The proline content, SOD and CAT activities, and ·OH scavenging capacity were enhanced in G. przewalskii under osmotic stress. RNA-sequencing of G. przewalskii generated 44.51 Gb clean reads, which were assembled into 102,191 Unigenes and 30,809 Unigenes were successfully annotated. Comparative analysis identified 3,015 differentially expressed genes under osmotic stress. There were 2,134 and 1,739 DEGs enriched in 47 GO secondary categories and 129 KEGG pathways, respectively. 2 up-regulated DEGs were annotated to P5CS, a key enzyme in the biosynthesis of proline. 32 DEGs were annotated to various antioxidases and antioxidants. 81 DEGs were annotated to 8 plant hormone signaling pathways, in which the auxin and ABA signaling pathways exhibited dominant enrichment. 150 DEGs were annotated to 35 transcription factor families with the abundant enrichment of TF families containing WRKY, bZIP, ERF, bHLH, MYB, and NAC.ConclusionsHigh forage quality and drought stress tolerance were observed in G. przewalskii. In response to drought stress, G. przewalskii orchestrates reactive oxygen species scavenging, proline biosynthesis, and other intricate physiological processes, with substantial contributions from plant hormones and transcription factors. This study provides new insights into the forage quality and the mechanisms involved in drought adaptation of G. przewalskii, offering a foundation for its conservation and sustainable utilization.

Comparative transcriptome analysis reveals the key role of photosynthetic traits in the formation of differences in photothermal sensitivity in tobacco

BackgroundThe photothermal sensitivity of tobacco refers to how tobacco plants respond to variations in the photothermal conditions of their growth environment. The degree of this sensitivity is crucial for determining the optimal planting regions for specific varieties, as well as for improving the quality and yield of tobacco leaves. However, the precise mechanisms underlying the development of photothermal sensitivity in tobacco remain unclear.ResultsIn this study, two tobacco varieties with significant differences in sensitivity, previously selected using a photothermal sensitivity model, were chosen as materials. Two experimental sites with considerable differences in photothermal conditions were selected for planting. The aim was to comparatively analyze the changes in agronomic traits, biomass, and physiological indices of the varieties under different experimental conditions, as well as to conduct transcriptome analyses. The transcriptome results revealed significant enrichment of differentially expressed genes (DEGs) related to photosynthesis, plant hormone signal transduction, and flavonoid biosynthesis pathways. In the photosynthesis and plant hormone signaling pathways, genes such as Lhcb, aldo, AUX/IAA, and SAUR were significantly upregulated. This upregulation promoted photosynthetic efficiency by enhancing the process of photosynthesis. However, this promotion also led to the increased production of harmful substances such as hydrogen peroxide and superoxide radicals, which can damage cellular structure and function. In the flavonoid biosynthesis pathway, genes such as FLS, CHI, and PAL were significantly upregulated, which enhanced the plant’s antioxidant capacity. This effectively mitigated the harmful effects of oxidative stress, helping to maintain normal photosynthetic function.ConclusionThe findings of this study suggest that the photosynthetic capacity of tobacco plants is enhanced through the coordinated regulation of the photosynthesis, plant hormone signaling, and flavonoid biosynthesis pathways. This enhancement plays a pivotal role in modulating the plants’ photothermal adaptability, ultimately contributing to variations in their photothermal sensitivity.

Multi-omics analysis reveals the regulatory mechanism of branching development in Quercus fabri.

The ability of axillary meristems to form axillary buds and subsequently develop into branches is influenced by phytohormones, environmental conditions, and genetic factors. The main trunk of Quercus fabri is prone to branching, which not only impacts the appearance and density of the wood and significantly reduces the yield rate. This study conducted transcriptomic, proteomic, and metabolomic analyses on three stages of axillary bud development in Q. fabri. A total of 12,888 differentially expressed genes (DEGs), 8193 differentially accumulated proteins (DAPs), and 1788 differentially accumulated metabolites (DAMs) were identified through comparisons among the stages and subjected to multi-omics joint analysis. Conduct interaction network analysis on DEGs and DAPs to identify the significant transcription factor family (AP2/ERF) involved in the regulation of axillary bud development. Furthermore, KEGG enrichment analysis of DEGs, DAPs and DAMs indicated significant enrichment in plant hormone signaling pathways. The analysis of endogenous hormone levels and qRT-PCR results for pathway genes demonstrated that the expression levels of IAA and tZ significantly increased during late developmental stages, whereas the expression levels of ABA, ACC and JA significantly decreased. In summary, these findings contribute to a comprehensive understanding of the regulatory networks underlying the branching development of Q. fabri. SIGNIFICANCE: Q. fabri exhibits robust vegetative growth, and its primary trunk is prone to branching, significantly influencing the wood yield rate. Through a joint analysis of transcriptomics, proteomics, and metabolomics, we comprehensively examined the regulatory network governing the axillary bud development of Q. fabri. Our findings revealed the crucial roles of the AP2/ERF transcription factor family and plant hormone signal transduction pathways in branch development. These insights contribute to a deeper understanding of the mechanisms regulating branch development.

Transcriptional Analysis of Tissues in Tartary Buckwheat Seedlings Under IAA Stimulation.

Background:Fagopyrum tataricum, commonly referred to as tartary buckwheat, is a cultivated medicinal and edible crop renowned for its economic and nutritional significance. Following the publication of the buckwheat genome, research on its functional genomics across various growth environments has gradually begun. Auxin plays a crucial role in many life processes. Analyzing the expression changes in tartary buckwheat after IAA treatment is of great significance for understanding its growth and environmental adaptability. Methods: This study investigated the changes in auxin response during the buckwheat seedling stage through high-throughput transcriptome sequencing and the identification and annotation of differentially expressed genes (DEGs) across three treatment stages. Results: After IAA treatment, there are 3355 DEGs in leaves and 3974 DEGs in roots identified. These DEGs are significantly enriched in plant hormone signaling, MAPK signaling pathways, phenylpropanoid biosynthesis, and flavonoid biosynthesis pathways. This result suggests a notable correlation between these tissues in buckwheat and their response to IAA, albeit with significant differences in response patterns. Additionally, the identification of tissue-specific expression genes in leaves and other tissues revealed distinct tissue variations. Conclusions: Following IAA treatment, an increase in tissue-specific expression genes observed, indicating that IAA significantly regulates the growth of buckwheat tissues. This study also validated certain genes, particularly those in plant hormone signaling pathways, providing a foundational dataset for the further analysis of buckwheat growth and tissue development and laying the groundwork for understanding buckwheat growth and development.

Transcriptomic and metabolomic analysis reveal differentially expressed genes and metabolic pathways in bermudagrass under drought stress

AbstractDrought stress poses a significant challenge to turfgrass growth, particularly in the regions like southern United States, where bermudagrass (Cynodon sp.) is widely used for lawns and sports fields. Drought stress disrupts physiological processes, leading to reduced water availability, impaired photosynthesis, and oxidative stress. To understand the bermudagrass response to drought, we investigated the physiological differences and characterized the gene expression and metabolite profiles in two bermudagrass genotypes, TifTuf and Premier. Physiological measurements showed significant variations in green cover percentage, visual quality, and relative water content between the two genotypes. RNA sequencing revealed extensive gene expression changes, with differentially expressed genes that were upregulated in both genotypes. Gene ontology (GO) analysis highlighted biological processes such as transcription regulation, lipid metabolism, and cellular structure development pathways. KEGG pathway analysis indicated that TifTuf had significant changes in galactose metabolism, carotenoid biosynthesis, and plant hormone signal transduction pathways, while Premier showed enrichment in plant hormone signaling, lipid metabolism, and secondary metabolite biosynthesis pathways. Metabolomic analysis provided insights into metabolic reprogramming due to drought stress. Principal component analysis revealed distinct metabolic patterns between control and drought‐stressed samples, with both genotypes showing substantial alterations. Differential metabolite analysis identified key metabolites associated with stress adaptation, including the phytohormone ABA and various amino acids. This analysis elucidates the intricate physiological and molecular mechanisms underlying drought tolerance in bermudagrass genotypes. These findings enhance the understanding of drought stress adaptation strategies in bermudagrass and offer valuable insights for the development of drought‐tolerant genotypes.

Metabolomic and transcriptomic analyses reveal the regulation mechanism of postharvest light-induced phenolics accumulation in mango peel

Phenolics are important secondary metabolites and antioxidants in plants. Mango fruit accumulate abundant phenolic compounds, while the effect of light on the accumulation of different phenolic components in mango peel and the relevant molecular mechanism are still unknown. In this study, mature ‘Guifei’ mango fruit was subjected to postharvest UV-B/white light treatment, fruit peel was sampled for metabolomic and transcriptomic analyses. The results showed that light induced the accumulation of anthocyanins, flavonoids, and phenolics, thus increasing the antioxidant capacity in mango peel. A total of 1223 phenolic metabolites were detected in mango peel, 36 phenolic compounds were defined as key differentially accumulated metabolites (DAMs) regulated by light. Among the DAMs, the accumulation of 33 compounds was promoted by light, and 30 of these were flavonoids. Light up-regulated most phenolics biosynthesis and light signaling pathway genes and also regulated expression of plant hormone signaling pathway genes. Transcription factors (TFs) such as MYB, C2H2 and HSF were identified as candidates regulating phenolics biosynthesis in mango. Our findings not only provide information for commercial application of light in promoting mango fruit appearance and increasing phenolics content and antioxidant capacity, but also reveal important aspects of the molecular regulation of light-induced phenolics accumulation in mango peel.

Transcriptome Analysis Reveals the Crucial Role of Phenylalanine Ammonia-Lyase in Low Temperature Response in Ammopiptanthus mongolicus.

Background: Ammopiptanthus mongolicus is a rare temperate evergreen shrub with high tolerance to low temperature, and understanding the related gene expression regulatory network can help advance research on the mechanisms of plant tolerance to abiotic stress. Methods: Here, time-course transcriptome analysis was applied to investigate the gene expression network in A. mongolicus under low temperature stress. Results: A total of 12,606 differentially expressed genes (DEGs) were identified at four time-points during low temperature stress treatment, and multiple pathways, such as plant hormones, secondary metabolism, and cell membranes, were significantly enriched in the DEGs. Trend analysis found that the expression level of genes in cluster 19 continued to upregulate under low temperatures, and the genes in cluster 19 were significantly enriched in plant hormone signaling and secondary metabolic pathways. Based on the transcriptome data, the expression profiles of the genes in abscisic acid, salicylic acid, and flavonoid metabolic pathways were analyzed. It was found that biosynthesis of abscisic acid and flavonoids may play crucial roles in the response to low temperature stress. Furthermore, members of the phenylalanine ammonia-lyase (PAL) family in A. mongolicus were systematically identified and their structures and evolution were characterized. Analysis of cis-acting elements showed that the PAL genes in A. mongolicus were closely related to abiotic stress response. Expression pattern analysis showed that PAL genes responded to various environmental stresses, such as low temperature, supporting their involvement in the low temperature response in A. mongolicus. Conclusions: Our study provides important data for understanding the mechanisms of tolerance to low temperatures in A. mongolicus.

Decoding the Impact of a Bacterial Strain of Micrococcus luteus on Arabidopsis Growth and Stress Tolerance.

Microbes produce various bioactive metabolites that can influence plant growth and stress tolerance. In this study, a plant growth-promoting rhizobacterium (PGPR), strain S14, was identified as Micrococcus luteus (designated as MlS14) using de novo whole-genome assembly. The MlS14 genome revealed major gene clusters for the synthesis of indole-3-acetic acid (IAA), terpenoids, and carotenoids. MlS14 produced significant amounts of IAA, and its volatile organic compounds (VOCs), specifically terpenoids, exhibited antifungal activity, suppressing the growth of pathogenic fungi. The presence of yellow pigment in the bacterial colony indicated carotenoid production. Treatment with MlS14 activated the expression of β-glucuronidase (GUS) driven by a promoter containing auxin-responsive elements. The application of MlS14 reshaped the root architecture of Arabidopsis seedlings, causing shorter primary roots, increased lateral root growth, and longer, denser root hairs; these characteristics are typically controlled by elevated exogenous IAA levels. MlS14 positively regulated seedling growth by enhancing photosynthesis, activating antioxidant enzymes, and promoting the production of secondary metabolites with reactive oxygen species (ROS) scavenging activity. Pretreatment with MlS14 reduced H2O2 and malondialdehyde (MDA) levels in seedlings under drought and heat stress, resulting in greater fresh weight during the post-stress period. Additionally, exposure to MlS14 stabilized chlorophyll content and growth rate in seedlings under salt stress. MlS14 transcriptionally upregulated genes involved in antioxidant defense and photosynthesis. Furthermore, genes linked to various hormone signaling pathways, such as abscisic acid (ABA), auxin, jasmonic acid (JA), and salicylic acid (SA), displayed increased expression levels, with those involved in ABA synthesis, using carotenoids as precursors, being the most highly induced. Furthermore, MlS14 treatment increased the expression of several transcription factors associated with stress responses, with DREB2A showing the highest level of induction. In conclusion, MlS14 played significant roles in promoting plant growth and stress tolerance. Metabolites such as IAA and carotenoids may function as positive regulators of plant metabolism and hormone signaling pathways essential for growth and adaptation to abiotic stress.

Understanding cold stress response mechanisms in plants: an overview.

Low-temperature stress significantly impacts plant growth, development, yield, and geographical distribution. However, during the long-term process of evolution, plants have evolved complicated mechanisms to resist low-temperature stress. The cold tolerance trait is regulated by multiple pathways, such as the Ca2+ signaling cascade, mitogen-activated protein kinase (MAPK) cascade, inducer of CBF expression 1 (ICE1)-C-repeat binding factor (CBF)-cold-reulated gene (COR) transcriptional cascade, reactive oxygen species (ROS) homeostasis regulation, and plant hormone signaling. However, the specific responses of these pathways to cold stress and their interactions are not fully understood. This review summarizes the response mechanisms of plants to cold stress from four aspects, including cold signal perception and transduction, ICE1-CBF-COR transcription cascade regulation, ROS homeostasis regulation and plant hormone signal regulation. It also elucidates the mechanism of cold stress perception and Ca2+ signal transduction in plants, and proposes the important roles of transcription factors (TFs), post-translational modifications (PTMs), light signals, circadian clock factors, and interaction proteins in the ICE1-CBF-COR transcription cascade. Additionally, we analyze the importance of ROS homeostasis and plant hormone signaling pathways in plant cold stress response, and explore the cross interconnections among the ICE1-CBF-COR cascade, ROS homeostasis, and plant hormone signaling. This comprehensive review enhances our understanding of the mechanism of plant cold tolerance and provides a molecular basis for genetic strategies to improve plant cold tolerance.

Genome-wide analysis of non-coding RNA reveals the role of a novel miR319c for tuber dormancy release process in potato

Abstract Tuber dormancy and sprouting are significant for potato cultivation, storage, and processing. Although the substantial role of miRNAs in some biological processes has been recognized, the critical role of miRNA in breaking potato tuber dormancy is not well understood to date. In this investigation, we expand research on miRNA-mediated gene regulation in tuber dormancy release. In this work, 204 known and 192 novel miRNAs were identified. 136 differentially expressed miRNAs (DE-miRNAs) were also screened out, of which 56 DE-miRNAs were regulated by temperature during tuber dormancy release. Additionally, degradome sequencing revealed that 821 target genes for 202 miRNAs were discovered. Among them, 63 target genes and 48 miRNAs were predicted to be involved in plant hormone signaling pathways. This study used degradome sequencing, tobacco co-transformation system, and GUS staining technology to confirm that stu-miR319c can target StTCP26 and StTCP27 and effectively suppress their expression. The transgenic approach exhibited that stu-miR319c overexpressed tubers sprouted in advance, while silent expression of stu-miR319c showed delayed sprouting. Treatment of wild-type tubers with exogenous MeJA revealed that 1 mg/L MeJA significantly broke dormancy and enhanced potato sprouting ability. Furthermore, transgenic tubers revealed variance in JA content and relative expression of genes associated with JA synthesis pathway, including StAOC, StLOX2, and StLOX4, suggesting that the miR319c may participate in the JA pathway to regulate tuber dormancy release. In summary, our research offers evidence that miRNA regulates potato dormancy release and supports the idea that stu-miR319c is a unique epigenetic regulator for dormancy-sprouting transition in potatoes.

Functions and mechanisms of CDPKs in plant responses to abiotic stress

Calcium-dependent protein kinases (CDPKs/CPKs) are members of the Ca2+-sensitive Ser/Thr protein kinase family and play a crucial role in plant growth and development and responses to abiotic stress. CDPKs are capable of rapidly sensing changes in intracellular Ca2+ signals and recognizing and phosphorylating specific substrates, thereby transmitting and amplifying Ca2+ signal cascades downstream. They are involved in plant responses to stress conditions such as drought, saline-alkali stress, and injuries and regulate plant growth and development, gene expression, ion channel activity, and stomatal movement. The autophosphorylation of CDPKs can affect their activities and substrate specificity. CDPKs have the ability to bind to and phosphorylate multiple substrates. In addition to participating in respiratory burst oxidase homolog (RBOH), mitogen-activated protein kinase (MAPK), and plant hormone signaling pathways, CDPKs can also bind to 14-3-3 proteins, which enables the regulation of plant responses to stress and promotes plant growth and development. This paper summarized the research findings on the discovery, structure, classification, and roles of CDPKs in plant responses to stress and proposed the future research directions, aiming to provide the genetic resources and a theoretical basis for improving the stress tolerance of crops.

The combined analysis of transcriptome and phytohormone provides new insights into signaling mechanism for lateral root formation of tea plant (Camellia sinensis)

The growth and development of lateral roots (LRs) determine the nutrient absorption and environmental adaptability of tea plant, playing a crucial role in the economic efficiency of tea plantations. However, the molecular mechanisms underlying the formation of LRs in tea plant remain unreported. In this study, we established a LRs induction system in tea plants by exogenously adding N-1-naphthylphthalamic acid (NPA) and naphthaleneacetic acid (NAA). The molecular mechanisms of LRs formation were analyzed through transcriptomics and endogenous hormone measurements. Results showed that NAA treatment could counteract the inhibitory effect of NPA on LRs formation and promote the generation of LRs in tea plant. The addition of exogenous NAA reduced the levels of auxin and zeatin in the root tips while increasing the content of abscisic acid (ABA). Transcriptomic analysis at four time points (2, 6, 12, and 24 h) after NAA vs. MOCK treatment revealed 78 different expression genes (DEGs) associated with plant hormone signaling pathways. Among these, the auxin signaling pathway was the most significant in responding to the LRs formation in tea plant. Weighted Gene Co-Expression Network Analysis (WGCNA) identified the Mitogen-Activated Protein Kinases (MAPK) signaling pathway as responsive to NAA treatment, participating in the formation of LRs in tea plant. This study provides potential signaling pathways for the investigation of LRs formation in tea plant and identifies candidate genes for further research into tea plant root system architecture (RSA).

Development and drought escape response in Arabidopsis thaliana are regulated by AtPLC1 in response to abscisic acid.

AtPLC1 plays a critical role in plant growth, development, and response to drought stress. Phosphoinositide-specific phospholipase C (PI-PLC) hydrolyzes substrates to generate secondary messengers crucial for plant growth, development, and stress responses. Drought escape (DE) response is an adaptive strategy that plants employ under drought conditions. The expression levels of the flower meristem-specific gene APETALA 1 and flowering regulatory genes FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 were downregulated in plc1, and FLOWERING LOCUS C was upregulated. The flowering time of the plc1flc double mutant was earlier than that of the wild type. Transcriptome analysis revealed that the Gene Ontology of differentially expressed genes (DEGs) was enriched in abscisic acid (ABA) response signaling, and Kyoto Encyclopedia of Genes and Genomes analysis revealed differential gene expression annotated to plant hormone signaling pathways. Our experiments show that AtPLC1 is upregulated by ABA in Arabidopsis. Under ABA induction and water stress, wild-type plants exhibit a DE response, and the DE response in plc1 disappears. Expression levels of ABA signaling pathway transcription factors ABA-responsive element-binding factors 3 (ABF3) and ABF4 were downregulated in plc1. In conclusion, our study suggests that AtPLC1 participates in regulating plant growth and development and participates in the DE response through the regulation of ABA signaling pathway transcription factors ABF3/ABF4. The study enhances our comprehension of the role of AtPLC1 in plant development and drought stress, providing a theoretical foundation for further investigation into DE responses.

Understanding of Plant Salt Tolerance Mechanisms and Application to Molecular Breeding.

Soil salinization is a widespread hindrance that endangers agricultural production and ecological security. High salt concentrations in saline soils are primarily caused by osmotic stress, ionic toxicity and oxidative stress, which have a negative impact on plant growth and development. In order to withstand salt stress, plants have developed a series of complicated physiological and molecular mechanisms, encompassing adaptive changes in the structure and function of various plant organs, as well as the intricate signal transduction networks enabling plants to survive in high-salinity environments. This review summarizes the recent advances in salt perception under different tissues, physiological responses and signaling regulations of plant tolerance to salt stress. We also examine the current knowledge of strategies for breeding salt-tolerant plants, including the applications of omics technologies and transgenic approaches, aiming to provide the basis for the cultivation of salt-tolerant crops through molecular breeding. Finally, future research on the application of wild germplasm resources and muti-omics technologies to discover new tolerant genes as well as investigation of crosstalk among plant hormone signaling pathways to uncover plant salt tolerance mechanisms are also discussed in this review.

Transcriptomic Insights into Salt Stress Response in Two Pepper Species: The Role of MAPK and Plant Hormone Signaling Pathways.

Salt stress imposes significant plant limitations, altering their molecular, physiological, and biochemical functions. Pepper, a valuable herbaceous plant species of the Solanaceae family, is particularly susceptible to salt stress. This study aimed to elucidate the physiological and molecular mechanisms that contribute to the development of salt tolerance in two pepper species (Capsicum baccatum (moderate salt tolerant) and Capsicum chinense (salt sensitive)) through a transcriptome and weighted gene co-expression network analysis (WGCNA) approach to provide detailed insights. A continuous increase in malondialdehyde (MDA) and hydrogen peroxide (H2O2) levels in C. chinense and higher activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) in C. baccatum indicated more tissue damage in C. chinense than in C. baccatum. In transcriptome analysis, we identified 39 DEGs related to salt stress. Meanwhile, KEGG pathway analysis revealed enrichment of MAPK and hormone signaling pathways, with six DEGs each. Through WGCNA, the ME.red module was identified as positively correlated. Moreover, 10 genes, A-ARR (CQW23_24856), CHIb (CQW23_04881), ERF1b (CQW23_08898), PP2C (CQW23_15893), ABI5 (CQW23_29948), P450 (CQW23_16085), Aldedh1 (CQW23_06433), GDA (CQW23_12764), Aldedh2 (CQW23_14182), and Aldedh3 (CQW23_11481), were validated by qRT-PCR. This study provides valuable insights into the genetic mechanisms underlying salt stress tolerance in pepper. It offers potential targets for future breeding efforts to enhance salt stress resilience in this crop.

Physiological characteristics and transcriptomic analysis of response patterns of Gynura divaricata (L.) DC. cultured in vitro under NaCl stress

Soil salinity, a major environmental stress, restricts agricultural production worldwide. Gynura divaricata (L.) DC. is widely cultivated on tropical islands in China and has both edible and medicinal value. NaCl stress and growth indicators, antioxidant enzyme activity, as well as MDA, proline, and soluble sugar content, were determined. Based on the transcriptomic data of tissue-cultured G. divaricata plantlets grown in control (0 mM NaCl) and salt stress (50 and 200 mM NaCl) conditions, gene expression patterns were examined. KEGG enrichment analysis of differentially expressed genes indicated significant enrichment of plant hormone signaling, MAPK signaling, and starch and sucrose metabolism pathways. These findings allowed key biological pathways and salt stress-responsive genes to be identified, thus providing a molecular basis for breeding salt-tolerant G. divaricata varieties. This transcriptomic analysis revealed a complex tolerance mechanism of G. divaricata in response to NaCl, laying a foundation for screening and cloning key genes related to NaCl tolerance and studying their interactions. These findings would allow the molecular basis of NaCl tolerance to be explored, with the aim of breeding NaCl-tolerant varieties.

Transcriptome analysis reveals candidate genes for different root types of alfalfa (Medicago sativa) after water stress induced by PEG-6000

BackgroundWe aimed to gain insight into the response mechanism of alfalfa (Medicago sativa) to drought stress by recognizing and analyzing drought-responsive genes in the roots of different root types of alfalfa. The rhizomatous-rooted M. sativa cv.‘Qingshui’ (QS), tap-rooted M. sativa cv.‘Longdong’ (LD), and creeping-rooted M. varia cv. ‘Gongnong No. 4’ (GN) were used to analyze the transcriptome information and physiological characteristics of the root systems of the cultivars under simulated drought stress using PEG-6000.ResultsIt was found that aridity caused a significant increase in the content of osmotic stress substances and antioxidant enzyme activity. The content of malondialdehyde (MDA) in QS was lower than that in LD and GN under moisture stress, indicating a stronger accumulation capacity of osmotic regulatory substances. Based on sequencing results, 14,475, 9336, and 9243 upregulated DEGs from QS, LD, and GN were annotated into 26, 29, and 28 transcription factor families, respectively. QS showed more DEGs than LD and GN. KEGG enrichment analysis identified that DEGs were significantly enriched in metabolic pathways such as amino acid biosynthesis, phenylpropanoid biosynthesis, plant hormone signaling transduction, and MAPK pathways. This suggests a strong correlation between these pathways and drought stress. The results also show that genes associated with ABA hormone signaling (MS. gene93372, MS. gene072046, and MS. gene012975) are crucial for plant’s adaptation to drought stress.ConclusionsThese genes, such as serine/threonine protein kinases and abscisic acid receptors, play a crucial role in plant hormone signaling and MAPK pathways. They could serve as potential candidate genes for drought resistance research in alfalfa, providing a molecular foundation for studying drought resistance.Graphical

Transcriptomic analyses provide molecular insight into the cold stress response of cold-tolerant alfalfa

BackgroundDaye No.3 is a novel cultivar of alfalfa (Medicago sativa L.) that is well suited for cultivation in high-altitude regions such as the Qinghai‒Tibet Plateau owing to its high yield and notable cold resistance. However, the limited availability of transcriptomic information has hindered our investigation into the potential mechanisms of cold tolerance in this cultivar. Consequently, we conducted de novo transcriptome assembly to overcome this limitation. Subsequently, we compared the patterns of gene expression in Daye No. 3 during cold acclimatization and exposure to cold stress at various time points.ResultsA total of 15 alfalfa samples were included in the transcriptome assembly, resulting in 141.97 Gb of clean bases. A total of 441 DEGs were induced by cold acclimation, while 4525, 5016, and 8056 DEGs were identified at 12 h, 24 h, and 36 h after prolonged cold stress at 4 °C, respectively. The consistency between the RT‒qPCR and transcriptome data confirmed the accuracy and reliability of the transcriptomic data. KEGG enrichment analysis revealed that many genes related to photosynthesis were enriched under cold stress. STEM analysis demonstrated that genes involved in nitrogen metabolism and the TCA cycle were consistently upregulated under cold stress, while genes associated with photosynthesis, particularly antenna protein genes, were downregulated. PPI network analysis revealed that ubiquitination-related ribosomal proteins act as hub genes in response to cold stress. Additionally, the plant hormone signaling pathway was activated under cold stress, suggesting its vital role in the cold stress response of alfalfa.ConclusionsUbiquitination-related ribosomal proteins induced by cold acclimation play a crucial role in early cold signal transduction. As hub genes, these ubiquitination-related ribosomal proteins regulate a multitude of downstream genes in response to cold stress. The upregulation of genes related to nitrogen metabolism and the TCA cycle and the activation of the plant hormone signaling pathway contribute to the enhanced cold tolerance of alfalfa.

Comprehensive Review on Bimolecular Fluorescence Complementation and Its Application in Deciphering Protein-Protein Interactions in Cell Signaling Pathways.

Signaling pathways are responsible for transmitting information between cells and regulating cell growth, differentiation, and death. Proteins in cells form complexes by interacting with each other through specific structural domains, playing a crucial role in various biological functions and cell signaling pathways. Protein-protein interactions (PPIs) within cell signaling pathways are essential for signal transmission and regulation. The spatiotemporal features of PPIs in signaling pathways are crucial for comprehending the regulatory mechanisms of signal transduction. Bimolecular fluorescence complementation (BiFC) is one kind of imaging tool for the direct visualization of PPIs in living cells and has been widely utilized to uncover novel PPIs in various organisms. BiFC demonstrates significant potential for application in various areas of biological research, drug development, disease diagnosis and treatment, and other related fields. This review systematically summarizes and analyzes the technical advancement of BiFC and its utilization in elucidating PPIs within established cell signaling pathways, including TOR, PI3K/Akt, Wnt/β-catenin, NF-κB, and MAPK. Additionally, it explores the application of this technology in revealing PPIs within the plant hormone signaling pathways of ethylene, auxin, Gibberellin, and abscisic acid. Using BiFC in conjunction with CRISPR-Cas9, live-cell imaging, and ultra-high-resolution microscopy will enhance our comprehension of PPIs in cell signaling pathways.

Efficient In Vitro Regeneration System and Comparative Transcriptome Analysis Offer Insight into the Early Development Characteristics of Explants from Cotyledon with Partial Petiole in Small-Fruited Pepper (Capsicum annuum).

In our research, we utilized six small-fruited pepper germplasms as materials, selected cotyledons with the petiole and hypocotyls as explants, and conducted in vitro regeneration studies. Our outcomes specify that the most suitable explant is cotyledon with the petiole, and the suitable genotype is HNUCA341. The optimal medium for inducing and elongating adventitious buds for this genotype is Murashige and Skoog medium (MS) + 9.12 μM Zeatin (ZT) + 0.57 μM 3-Indoleacetic acid (IAA), with a bud induction rate of 44.4%. The best rooting induction medium is MS + 1.14 μM IAA, with a rooting rate of 86.7%. Research on the addition of exogenous hormones has revealed that the induction speed of buds in small-fruited pepper (HNUCA341) in the combination of ZT and IAA hormones (abbreviated as ZI) is quicker, and the induction effect is better. The histological observations indicate that ZI treatment accelerates the initiation of explant division and differentiation, causing a shorter duration of vascular-bundle tissue production. The plant hormone signaling pathway was significantly enriched by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, including ARR9 (LOC107843874, LOC107843885), ARR4 (LOC107848380, LOC107862455), AHK4 (LOC107870540), AHP1 (LOC107839518), LAX2 (LOC107846008), SAUR36 (LOC107852624), IAA8 (LOC107841020), IAA16 (LOC107839415), PYL4 (LOC107843441), and PYL6 (LOC107871127); these significantly enriched genes may be associated with in vitro regeneration. In addition, the carbon metabolism pathway and plant mitogen-activated protein kinase (MAPK) signaling pathway are also significantly enriched in KEGG. The results of the Gene Ontology (GO) analysis revealed that differentially expressed genes related to carbon metabolism and fixation, photosynthesis and MAPK signaling pathways were upregulated under ZI treatment. It was found that they might be associated with enhanced regeneration in vitro. Furthermore, we also screened out differentially expressed transcription factors, primarily from the MYB, bHLH, AP2/ERF, and NAC families. Overall, our work accumulated important data for the in-depth analysis of the molecular mechanism of in vitro regeneration of pepper, and provides valuable germplasm for establishing an efficient stable pepper genetic-transformation system based on tissue culture.